At a glance

This report contains visualisations of statistics that can help in understanding the results from the wf-human-variation workflow. Each section contains different plots or tables, and in general the results are broken down by sample. You can quickly jump to an individual section with the links in the header bar.

Sample total reads

6028432

Sample read N50

19726 bp

Sample mean coverage

17.157x

Summary

Metric Value Percentage
Reads 6,028,432
100.0%
Unmapped reads 18,121
0.3%
Bases 52,982,176,736
100.0%

Read statistics

This section displays the read statistics for the sample processed. The left plot shows the read quality (range cropped to 4-30) vs. the number of reads. The central plot shows the reald lenth vs. number of reads. The left plot shows the base yield above a given read length.

Depth of coverage

This section illustrates the depth of coverage of the reference genomes. The plot shows coverage vs. genomic position (note that the coordinates on the x-axis are the positions along the concatenated reference including all reference sequences in the respective reference file).

Software versions

Name Version
mosdepth 0.3.3

Workflow parameters

Key Value
help False
version False
disable_ping False
threads 4
aws_image_prefix None
aws_queue None
out_dir output
snp True
sv True
mod True
cnv False
str False
sv_benchmark False
sv_benchmark_vcf None
sv_benchmark_bed None
bam /proj/hpcdata/Mimir/shared/brynjar/nanopore/dna_met/8_d4921/merged.bam
ref /proj/hpcdata/Mimir/shared/brynjar/nanopore/human_var/gogn/Homo_sapiens.GRCh38.dna.primary_assembly.fa
bed None
bam_min_coverage 17
downsample_coverage False
downsample_coverage_target 60
downsample_coverage_margin 1.1
depth_window_size 25000
output_gene_summary False
haplocheck False
mitogenome None
ubam_map_threads 8
ubam_sort_threads 3
ubam_bam2fq_threads 1
annotation True
basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v4.2.0
clair3_model_path None
use_longphase False
sample_name 8_d492-1
ctg_name None
include_all_ctgs False
ref_pct_full 0.1
var_pct_full 0.7
GVCF False
base_err 0.001
gq_bin_size 5
snp_min_af 0.08
indel_min_af 0.15
vcf_fn None
min_contig_size 0
min_mq 5
min_cov 2
min_qual 2
refine_snp_with_sv True
tr_bed /proj/hpcdata/Mimir/shared/brynjar/nanopore/human_var/gogn/human_GRCh38_no_alt_analysis_set.trf.bed
min_sv_length 30
min_read_support auto
min_read_support_limit 2
cluster_merge_pos 150
sniffles_args None
use_qdnaseq False
qdnaseq_bin_size 500
modkit_args None
force_strand False
modkit_threads 4
sex XX
depth_intervals False
phased True
output_report True
output_xam_fmt cram
monochrome_logs False
validate_params True
show_hidden_params False
schema_ignore_params show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf,min_read_support,min_read_support_limit,fastq_only
wf {'name': 'wf-human-variation', 'template_version': '195cab5', 'example_cmd': ['--bam wf-human-variation-demo/demo.bam', '--basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom', '--mod', '--ref wf-human-variation-demo/demo.fasta', '--sample_name DEMO', '--snp', '--sv'], 'agent': None, 'e2l_base_tag': 'sha2b856c1f358ddf1576217a336bc0e9864b6dc0ed', 'e2l_snp_tag': 'sha17e686336bf6305f9c90b36bc52ff9dd1fa73ee9', 'e2l_sv_tag': 'shac591518dd32ecc3936666c95ff08f6d7474e9728', 'e2l_mod_tag': 'sha0253e9e9ba92aacc852ba376edefe8ff0932f71a', 'cnv_tag': 'sha428cb19e51370020ccf29ec2af4eead44c6a17c2', 'str_tag': 'shaa2f49ce57886426516eadd4048b6fdf9c22c7437', 'spectre_tag': 'sha5a2890023dc7a7899f47585103b4f5762fb9d1b3', 'snpeff_tag': 'sha313729d816872d70b410752001a0e2654eb88807', 'common_sha': 'sha338caea0a2532dc0ea8f46638ccc322bb8f9af48'}
outdir /proj/hpcdata/Mimir/shared/brynjar/nanopore/human_var/gogn/8_d492-1